The Darkness in the Doctor
by Gambit791
Summary: A work in progress set post The Big Bang but before series 6.  It's going to have a few  hopefully  interesting twists and I'm going to try and show a darker side of the Doctor than we're used to by the end of it.    Hope you enjoy.
1. Chapter 1

The Darkness in the Doctor

The familiar groan of the TARDIS echoed around Amy as she walked into the control room. "So, where are we off to today then? Rory wants to know what shoes to wear."

"Shoes? Shoes? I thought it was you women who were all for the shoes. What's he worrying about shoes for? That's what I love about you humans, whole universe of time and space on your doorstep and you worry about what shoes to wear," The Doctor exclaimed as he came bouncing down the gantry steps. "He wore out his best pair running around France when we bumped into Vincent. He's quite annoyed at you for that actually. Says he wants you to warn him when running will be involved," replied Amy, a smirk lighting up her pale face.

"Oh it's me, of course there'll be running involved. And lots of it. What's he moaning for, it's good for you. Keeps my hearts healthy anyway. Nothing like a good old morning run to clear the sinuses."

At this Rory's head poked around a corner, an indignant expression crossing his face. "It's not moaning. I just want to be prepared. That's the trouble with you, you're never prepared."

The Doctor looked up from the TARDIS console. "Where's the fun in that? Being prepared never works in this life. Never know what to expect. Make it up as you go along, that's the ticket." And with that he threw down the nearest lever, wrapped a bell with his knuckle several times and pressed a large blue button. "Right, let's get this old girl landed shall we, we haven't got all day." He paused, and with a bemused look he said, "Well actually we do I suppose, time machine and all that but still. Stop dilly-dallying Rory! Amy, you need to have him better trained." He pulled his jacket on.

"I'm not a pet!" exclaimed Rory.

"Well stop acting like one then or I'll dig out a lead. I'm sure I've got one somewhere around. Definitely had one when I saved that last Dodo. And that Velociraptor I kept for a while definitely needed walking regularly."

"You had a raptor?" inquired Amy.

"Oh yes, he was called Gerald. Friendly little thing, a bit...bitey. But we're all like that when we're peckish so no harm done."

"I don't bite when I'm hungry."

"Well that just shows a lack of spirit then, doesn't it Rory?" replied the Doctor, "Anyway, let's see what's outside. Geronimo, aye?"


	2. Chapter 2

The Darkness in the Doctor, Chapter 2

The TARDIS door swung open and the Doctor stepped out. There was a loud squelching noise. "Ah. A swamp planet. Not my favourite kind, but hey ho."

Amy laughed, "You're sinking."

"Strangely enough Amy, I had noticed that." The murky swamp-water was up to his thighs, "Well this is really going to ruin MY shoes, let alone the flimsy things you wear."

"Hang on, I'll go find a rope or something," replied Amy, and she disappeared.

"Maintenance corridor, third door on the right, second shelf down, behind the Pringles!" The Doctor shouted after her.

Rory looked out. "This is what I meant about being prepared you know."

"Oh shush, don't just stand there looking pretty, go check where we are. You should know how to do that by now."

"I'm back!" Amy threw a large red cable out into the swamp.

"Jolly good, I need to get out of here before my bow-tie is ruined. Swamps don't really look too kindly on fashion accessories." He grabbed the cable, "Right, give it tug then, you helpful little humans."

Rory and Amy both held on tightly to the cable and slowly pulled the Doctor out of the swamp. The mists curled up around him as if they didn't want to lose their latest would-be victim.

"That's better, back in the TARDIS. Did you find out where we are Rory?" The Doctor jumped up and brushed down his pants.

"It's just throwing up static." He pointed at the viewscreen.

The Doctor's brow creased in puzzlement, "Well that's a bit odd. Something's interfering with the old girl's circuits. Can't be having that now, can we."

"So what do we do? Leave?" Amy smirked, "Is the Time Lord scared of a bit of static?"

"Leave? Of course not. Strange swamp planet, mysterious static, frankly terrible ground conditions and a high chance of prevailing south-westerly winds and a spot of rain, at least according to the atmosphere reader." He pulled down another viewscreen, "We'll dress up for swamping and go find out what this place is."

"Dress up for swamping?" Rory didn't look happy with this idea.

"Yep, nice orange swampsuits, always useful in a swampy swamp such as this. I'll go find them."

The Doctor wandered off into the depths of the TARDIS.

"Ugh, I hate swamps," declared Rory, "They're so...muddy."

"When have you ever been to a swamp before?"

"Never. But my point remains." He replied.

"Shush and come here you daft muppet." She hugged him warmly, "Do you think we'll ever get tired of this life?"

"I'm quite tired to be honest."

"No, I mean seriously. Seeing the Universe. Do you think we'll ever leave the Doctor?" Her sparkling eyes looked up at him.

"Maybe. I don't know. We'll see I guess."

"Oh come on now, you can't ever get bored of little old me." The Doctor cannoned down the TARDIS steps in a large orange swampsuit. The light reflected off the yellow helmet into Amy's eyes.

"So that's a swampsuit?" asked Amy, "It's hardly the kind of thing you'd wear to a party."

"Well I don't know about you Pond, but I've not been to many parties in swamps. Apart from that smashing shindig on Kravola, but that was different." He gave each of them a suit, "Get these bad boys on, we've got some exploring to do."


	3. Chapter 3

Chapter 3

It was a short while later and the intrepid trio had suited up. The Doctor motioned towards the TARDIS doors, "Run along you two, go outside and do whatever it is you humans do nowadays."

"You sound like Rory's grandad," Amy giggled.

"You never know, I might be, wibbly-wobbly timey-wimey!" He playfully punched Rory on the arm, "What d'you think of that, sonny jim?"

"I don't even want to think about it," answered Rory forlornly.

"I'd make a brilliant grandad. Who else's grandad has something as cool as this?" he exclaimed, slapping the TARDIS console, "Now go on, get out there, I'll be out in a jiffy. Try not to miss me too much, I just need to check out this signal."

The TARDIS doors swung shut. The Doctor glanced at them, and then moved around to a blinking light on the far side of the console. "Morse code?" he mumbled, "I hate morse code. Too dotty." The light continued blinking. "H...E...L...L," he mouthed, "Hell? Oh dear...O. Oh, hello! I like hello, hello is good." He studied the light some more. "S...W...E...E...T...I...E," his brow furrowed, "Sweetie. Ah. Well, suddenly things got interesting."

Grey mist swirled around the dark blue edges of the TARDIS. The howls of strange, alien creatures sounded in the distance, and the glow of a far-off green moon glittered on the horizon. Amy shivered. "It's cold out here." She yelped and pointed at the sky, "What's that?" A silver line was moving across the sky, down from the heavens. As it streaked downwards, the sky seemed to tear open. The green moon flickered intensely. Rory held tightly onto Amy. "That doesn't look...good," he said, "In fact I'd say that looks bad. Very bad." Thunder rumbled, getting louder and louder as the streak of silver sped across the sky. The Doctor burst out of the TARDIS. "What the blazes is going on out here, the readings are off the sc-." His voice was drowned out by thunder, rumbling through the atmosphere like the sound of 10,000 starships. There were dark clouds forming in the sky, giving the eery impression of a silvery knife cutting through reality. The three of them stared upwards as the air seemed to tear, a static feeling coming over everything. The Doctor garppled in his coat, pulling out the sonic screwdriver. He checked his readings, looked up at Amy with a look of horror on his face, and he pushed her into the TARDIS. Everything went white.

Inside the TARDIS it was all red. A warning siren clanged, echoing through the huge interior. Amy screamed as she fell into the TARDIS, she looked behind her and heard the Docter shout, "This is wrong! Need to echo!" before he seemed to be whipped from the space before her and the doors slammed shut. Sparks shot from the TARDIS console as the central column heaved and groaned, the familiar sound of time travel surrounding Amy. "Doctor!" she screamed, throwing herself at the doors, but slamming against them in vain. More sparks flew from the console as a strange glow appeared on the walkway. Amy gasped as it's shape became clearer. It was a hologram of the Doctor. It spoke, "If passengers are seeing this message then the TARDIS has lost dimensional stability whilst I am not on board. Not a good idea. The automatic systems will attempt to keep her adrift and functioning for as long as possible but without proper control the ship will shut down in 36 hours. So unfortunately, Amelia Pond, you're on your own from here."


	4. Chapter 4

Chapter 4

Rory woke up. The fetid swamp water in which he had fallen had disappeared. He was in a concrete room with no windows. A small door was set in the corner of the room, but bars were across it. He realised he was on a bed. On another bed opposite him, the Doctor looked up.

"Ah, Rory, I see you've decided to join me, splendid."

"Where are we?" he groaned, "And where's Amy?"

"I thought you might ask that, but don't you worry, I have answers for both of those questions."

"Well answer me then. What's going on?"

"That's another question. Well done."

He paused. A sheepish expression crossed his face.

"Don't know, in the TARDIS. Don't know to question number three too. Isn't this exciting?"

"She's in the TARDIS? Are you sure?"

"Yes. I double checked. Would've triple checked if being transmatted here hadn't interrupted my busy social calendar," he pointed at the barred door, "We're trapped. Well...they think we're trapped. Whoever they are. Wizards probably. No, wizards would be silly; they're not big on concrete." He got up off the bed, and wandered over to the door.

"What are you talking about Doctor?"

"Didn't have the heart to sonic us out of here straight away, make it look to easy and then no-one will ever be any fun when I'm around," he smiled, "Come on you, now you're awake we can find out what's going on and be back in time for tea. I quite fancy some tea." He whipped the sonic screwdriver out of his jacket and buzzed it at the door. The bars slid back and it swung open.

"No guards? Amateurs. Let's go Mr Pond, that little display in the swamp looked far too much like an interdimensional rift for my liking; I expect I've got quite a bit of work to do."

The cloister bell continued to sound throughout the TARDIS. Amy was panicking, swiftly moving around the console trying to use the knowledge she'd picked up on her travels with the Doctor to work out what was going on. "Come on TARDIS, don't just strand me here." The engines groaned in an unfamiliar way. Then suddenly, it stopped. Amy glanced at the monitor, and did a double-take. "Stormcage Prison Facility?" she gasped. There was a knock at the door. Amy ran towards it and tore the doors open. River Song stood illuminated in the gap. "Hello Amy. What trouble has he got himself into this time?"

The Doctor and Rory jogged through concrete corridors, searching for some clue as to where they were. The Doctor kept looking at his phone. "No signal? This thing should get signal anywhere. Well, anywhere apart from Fulham but that's normal." They came to a large black door, and on it were the words, "Strikecast Seven."

"A Strikecast facility? Well that narrows things down a bit."

"Doctor, what's a Strikecast facility?" asked Rory.

"Cloning. Well. Like cloning. Sort of. Okay, not remotely like cloning but it'll probably help if you just think of it as cloning."

"Oh. Okay."

"Very fashionable round about the 29th century, so I'd probably hazard a guess that that's when we are," he knocked on the door, "Well, let's have a look-see in here then, shall we?"


	5. Chapter 5

Chapter 5

"River?" Amy ran up to her and hugged her, "The TARDIS went mad. I lost Rory, and the Doctor. There was a gap in the sky!"

"Slow down Amy, tell me what happened."

"We were on a swamp planet. The Doctor wasn't sure where. But just as we were leaving the TARDIS things went weird."

"That doesn't sound good. He can never go anywhere nice and quiet can he? But that's why we stay with him." River walked into the TARDIS and up to the console. Amy followed her.

"So what do we do?" asked Amy.

"We need to find the Doctor. I have a bad feeling about all of this."

"And we do that how? It's not like he's tagged or anything."

"No, but the Doctor is unique in the Universe, it's surprisingly easy to find him. And there's one place that will definitely be able to track him down." She pulled some levers on the console and the central column began it's familiar wheezing.

"Where are we going then?"

"We're going to see the Shadow Proclamation. Oh he's going to hate me for involving them. I don't have much choice though."

Amy looked confused. "Who are they? I've never heard of them."

"You'd probably best think of them as intergalactic police. They've been keeping track of the Doctor ever since they realised he existed. He's a dangerous man to have wandering around."

"Don't I just know it..."

The Doctor knocked on the door again. "No answer. Probably nobody home then. Or they're all standing behind this door. With guns. Big guns if I'm any judge. Oh well." He swung the door open.

"Nothing," said Rory, "Nobody here. Just an empty room."

"Hmmm. Empty? Or full of invisible guards?" He buzzed the sonic screwdriver. Nothing happened.

"Wait, no, you're right Rory, nothing." He walked into the middle of the room, "How odd. You'd think they'd have guards. I do have a bit of a reputation for being tricky to keep locked up. I'm quite offended."

Suddenly the room shook. A klaxon roared into life, and a deep, booming voice was heard.

"Intruder alert. Intruder alert. Level 5 security breach in Power Processing. All drones protect the Oracle Device."

"Well seems this place is in a spot of bother. No wonder there are no guards. They're probably not that fussed about a couple of surface stragglers. Mustn't have realised who I am yet. Come along Mr Pond, we've got a crisis to find!"

"My name is Rory!"

Elsewhere in the facility, shadowy figures moved silently through smoky corridors. Several alien guards, tall and wearing blackened armour moved in front of them. Their auburn, scaly skin glistened in the little light there was.


	6. Chapter 6

Chapter 6

In the depths of space, a small asteroid floated. On it could be seen small buildings, lights, and close to the ground, people. In a large, hall-like structure, the groaning of the TARDIS began as the blue box materialised. River stepped out. A tall, pale man, robed entirely in black apart from the blood red crescent moon on his forehead, stepped forwards.

"You are not the Doctor." His words were slow and deliberate but a look of confusion passed his creased face.

"No. But I am his friend, and he trusts me. Well...most of the time. So should you."

"Why are you here?" He pointed at the TARDIS, "Why do you have his remarkable machine?"

Then Amy walked out of the TARDIS.

"I lost him. Something happened to the TARDIS. The Doctor and Rory, my husband, were outside when it happened. I couldn't stop it."

"The TARDIS was affected by another force. It made her become dimensionally unstable until it managed to track down a familiar presence in the time stream. It found me." River looked at the man, "I know you keep track of the Doctor. Ever since the Shadow Proclamation discovered he existed, you've wanted to know where he is. You're afraid of what he is capable of."

"He is a thorn in our side. He pays no attention to the rules. The Timelords are gone, he would do well to remember that."

"That man has saved the lives of everyone in this room many times! The universe owes him so much that it doesn't even realise! How dare you say that!"

"Help us find him," said Amy, "Tell us where he is."

Far across the universe, the Doctor was pondering.

"I do like pondering you know, Rory. Very under rated as a hobby. Nothing wrong with a good ponder." He was sat on a pile of boxes, legs crossed, beaming at his friend.

"Hello? There's a siren blaring at us! We've lost Amy! And the TARDIS! What are you sitting there grinning for?"

"Oh we're having fun! Amy is definitely in the TARDIS. Well, almost definitely. And the TARDIS is definitely not going to run into any trouble. Well, almost definitely. And that siren is definitely nothing to worry about. Well, almo-"

At that point the wall exploded, throwing them both to the ground.

Rory coughed through the smoke, "Owwww!"

"Two out of three ain't bad?" The Doctor catapulted towards the hole in the wall, "Let's go this way!"

"The Doctor is far from here on a planet that no longer exists."

"Well that narrows it down to an almost infinite number of planets, thank you. Could you be less useful?" River walked over to a star chart.

"You're very interested in the Katrodel system aren't you? There's a lot of processing power here going to piggy backing off local surveillance. Spying on the Doctor?"

"The affairs of the Proclamation are our own."

"That's a yes then. Come on Amy, let's go!"

"The Proclamation will prevent this. The Doctor cannot be allowed to interfere further with the universe."

"Hard cheese!" shouted Amy, as the TARDIS doors swung shut behind her.


	7. Chapter 7

Chapter 7

The smoke cleared. The Doctor fanned his way through the settling dust. Rory stumbled along behind him. "Is this safe, Doctor?"

"Oh probably. I wouldn't breathe too much of it in though if I were you."

"I kind of meant wandering blindly through a hole in a wall that wasn't there just a few minutes ago."

"Pfffffft, holes in walls are meant to be walked through Rory! They wouldn't be there otherwise." He pointed the sonic screwdriver through the hole, and it buzzed loudly.

"Well there's good news and bad news."

"Um…" Rory stuttered.

"Good news is there's somebody not too far through here. Bad news is they're surrounded by other somebodies who are heavily armed with somethings," The Doctor bounded through the whole, "Come along Pond."

The familiar groan of the TARDIS echoed through concrete halls. As the sound of materialisation faded, the door swung open and River Song marched out. "The moon of Katrodel IV, never been very important."

"Then why did someone bring the Doctor and Rory here? What happened to the swamp we were in?" asked Amy.

"Well Katrodel itself is probably the swamp planet. It's down there." River pointed towards the large green mass in the sky. Amy gasped.

"It's huge!"

"This is only a moon, what we're on now. There shouldn't be anything here, certainly no evolved life. This system is just too young." River looked around, and then tapped at the vortex manipulator on her wrist. "Whatever is going on here is playing havoc with this. Can't get any good readings."

"So what now?"

"We'll just have to find them the hard way. By looking!"

The Doctor and Rory scrambled over debris left from the explosion in the wall. They were in a dark room filled with electronic equipment. Cables dangled from the ceiling, others trailed the floor in an untidy mess. "So, a control room. I think. Could be anything really but I'll go with that."

Rory was looking worriedly down another corridor. He pointed to it. "Doctor…"

Two armed men walked out, with a hooded figure who seemed to be a prisoner.

"You should not be here. Return to your cell!"

"How rude. No, I don't think I will. You've brought my friend and I here by force, and I don't take kindly to force. Unless it's Star Wars, brilliant films, not so sure about the prequels but still." He pointed the sonic screwdriver at the guards, "Those helmets you're wearing probably have some kind of communication system in them, it would be a shame if I broke them." The Doctor slid the sonic to full power and both guards collapsed, clawing at their ears.

"Rory, grab her and let's go!"

"Her?"

"The hoody."

And with that he dashed down the corridor.

Somewhere in the dusty expanse of the moon's surface a lone, dark figure wandered towards the lone square outline of the TARDIS. Energy crackled off the figure, illuminating a thin frame. He raised a solitary hand towards the doors, lightning crackling along his grey skin. There was a sound. A finger clicked. A door swung open. A Doctor laughed.


End file.
